I want to perform pairwise alignment and get the resulting CIGAR string (Concise Idiosyncratic Gapped Alignment Report). A fuller description being here
The channel can emit insertions, deletions and substitution errors.
For example, if the input was AAGCT
Then the output could be AAAAGGC
Where there were the following errors in the following positions.
1, Insertion of A at first position 2, Insertion of A at second position 3, Insertion of G at the third position 4, Deletion of T at the last position
I want to know how I could obtain the CIGAR string given two sequences. In addition, could I use viterbi algorithm for this?